Marks lashed out at the process Wednesday, calling the Pro Bowl "a political thing" that shows the NFL is "not about players and their performances."
Marks was left off the initial Pro Bowl team that was released Tuesday night. He was voted an alternate for the all-star game, which will be played in Glendale, Arizona, in January.
Marks said he would accept an invitation to play in the game, but added that he's lost respect for it.
"I won't hold it in high regards like I used to," he said. "I don't get it. I don't understand it. It's more reputation than based on what you did on the field that season. It's a political thing. It shows that the NFL is all about money. It's not about players and their performances."
Marks has 8½ sacks this season, tied for second in the NFL among interior defensive linemen. Only Buffalo's Marcell Dareus has more (10).
Marks surely was hurt by playing for the small-market Jaguars (3-12) and on a losing team. He finished 13th at his position in fan voting, which makes up one-third of the ballot.
"You play for the guys and you play for the team to win, but the individual goal is to make it to the Pro Bowl," Marks said. "You hang your hat on that. If you have a great season, you're credited by a trip to the Pro Bowl. Now, I just won't hang my hat on that.
"I'll continue to play the way I've been playing, but it's not something that I'll hang my hat on each season. Sure if I'm called in, I'll go because it's huge for not only me, but it's (an honor) for your teammates, the coaches and your organization."
Marks leads the Jaguars in sacks. He also has 42 tackles, a forced fumble, a fumble recovery and one pass breakup. More than half of his 16Â½ career sacks have come this season.
Coach Gus Bradley said Marks deserves to be a Pro Bowler.
"I can't say enough good things about him," Bradley said. "I used him as an example to the team today about how he's internally motivated, and when you build a team full of guys that are internally motivated you have a really strong mindset and really strong team.
"I know what we believe in him and what our team thinks of him. He's a Pro Bowl player, just what he brings every day to our locker room, what he brings to practice and on the field."
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